9RKV | pdb_00009rkv

Agrobacterium phage 7-7-1 tail fibers

• PDB DOI: https://doi.org/10.2210/pdb9RKV/pdb
• EM Map EMD-54022: EMDB EMDataResource

• Classification: VIRUS
• Organism(s): Agrobacterium phage 7-7-1
• Mutation(s): No 


• Deposited: 2025-06-14 Released: 2025-12-10 
• Deposition Author(s): Noteborn, W.E.M., Hoeksma, T., Briegel, A.
• Funding Organization(s): Netherlands Organisation for Scientific Research (NWO)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.52 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Using cryogenic electron micrography methods to gain insight into structure and initial host attachment of the fagellotrophic bacteriophage 7-7-1

Noteborn, W.E.M., Hoeksma, T., Briegel, A.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 13-mer - A6B4C3 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 13-mer - A4B3C2D2E1F1 

Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - B2 Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - B2 

Biological assembly 1 assigned by authors and generated by (software)

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 430.33 kDa 
• Atom Count: 29,682 
• Modeled Residue Count: 4,038 
• Deposited Residue Count: 4,113 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Structural protein	A, B, I [auth C], J [auth D]	141	Agrobacterium phage 7-7-1	Mutation(s): 0
UniProt
Find proteins for J7FAF8 (Agrobacterium phage 7-7-1) Explore J7FAF8  Go to UniProtKB:  J7FAF8

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Structural protein	C [auth G], D [auth H], E [auth I], F [auth J], G [auth K], H [auth L]	298	Agrobacterium phage 7-7-1	Mutation(s): 0
UniProt
Find proteins for J7F9D4 (Agrobacterium phage 7-7-1) Explore J7F9D4  Go to UniProtKB:  J7F9D4

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative tail fiber	K [auth M], L [auth N], M [auth O]	587	Agrobacterium phage 7-7-1	Mutation(s): 0
UniProt
Find proteins for J7F8Z3 (Agrobacterium phage 7-7-1) Explore J7F8Z3  Go to UniProtKB:  J7F8Z3

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.52 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX
RECONSTRUCTION	cryoSPARC

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-12-10 
Deposition Author(s): Noteborn, W.E.M., Hoeksma, T., Briegel, A.

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Funding Organization	Location	Grant Number
Netherlands Organisation for Scientific Research (NWO)	Netherlands	184.034.014

Revision History  

• Version 1.0: 2025-12-10
  Type: Initial release